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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ), 'gf_id' => 'HOM05D001283', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001283' ), 'data_identifier' => 'HOM05D001283', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001283', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '488', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p40060' => 'bna', 'A04p04470' => 'bna', 'A05p17550' => 'bna', 'A05p37380' => 'bna', 'A06p00270' => 'bna', 'A08p00730' => 'bna', 'A08p00740' => 'bna', 'Aa31LG10G10500' => 'aar', 'Aa31LG10G1070' => 'aar', 'Aa31LG11G10880' => 'aar', 'Aa31LG8G770' => 'aar', 'Aa31sc238G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2471' => 'aag', 'Actinidia17293' => 'ach', 'Actinidia30431' => 'ach', 'Actinidia38604' => 'ach', 'Actinidia39355' => 'ach', 'AL1G63350' => 'aly', 'AL3G23580' => 'aly', 'AL3G25480' => 'aly', 'AL5G36610' => 'aly', 'AL6G30160' => 'aly', 'Aqoxy1G00438' => 'aox', 'Aqoxy2G02150' => 'aox', 'Aqoxy2G03159_Aqoxy2G03160' => 'aox', 'Aqoxy5G00595' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4LB3M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60QTDI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AVS37Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E8KUAX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F6WF27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HMW6IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J21882' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J65KEH' => 'arhy', 'AT1G55310' => 'ath', 'AT3G13570' => 'ath', 'AT3G55460' => 'ath', 'AT5G18810' => 'ath', 'ATR0487G002' => 'atr', 'ATR0559G043' => 'atr', 'ATR0559G204' => 'atr', 'ATR0737G103' => 'atr', 'Atru.chr12.439' => 'acertr', 'Atru.chr3.2360' => 'acertr', 'Atru.chr8.1219' => 'acertr', 'AUR62012095' => 'cqu', 'AUR62015293' => 'cqu', 'AUR62019180' => 'cqu', 'AUR62032735' => 'cqu', 'AUR62039371' => 'cqu', 'BcaB01g00098' => 'bca', 'BcaB02g08419' => 'bca', 'BcaB02g10830' => 'bca', 'BcaB04g16966' => 'bca', 'BcaB04g20989' => 'bca', 'BcaC01g01513' => 'bca', 'BcaC02g09759' => 'bca', 'BcaC08g44189' => 'bca', 'BolC1t05097H' => 'bol', 'BolC3t21574H' => 'bol', 'BolC3t21575H' => 'bol', 'BolC4t25255H' => 'bol', 'BolC5t34261H' => 'bol', 'BolC6t36101H' => 'bol', 'BolC6t36788H' => 'bol', 'BolC6t37849H' => 'bol', 'BraA01t04047Z' => 'bra', 'BraA04t16158Z' => 'bra', 'BraA05t20649Z' => 'bra', 'BraA05t22537Z' => 'bra', 'BraA06t23244Z' => 'bra', 'BraA08t32130Z' => 'bra', 'BraA08t32131Z' => 'bra', 'C01p51540' => 'bna', 'C03p92610' => 'bna', 'C04p36890' => 'bna', 'C05p55940' => 'bna', 'C06p10260' => 'bna', 'C06p15960' => 'bna', 'C06p26730' => 'bna', 'C08p11220' => 'bna', 'CANSAT11G2380' => 'cansat', 'CANSAT56G3091' => 'cansat', 'CANSAT56G4008' => 'cansat', 'CANSAT64G1377' => 'cansat', 'CANSAT78G1728' => 'cansat', 'CARHR044960' => 'chi', 'CARHR086530' => 'chi', 'CARHR088240' => 'chi', 'CARHR088250' => 'chi', 'CARHR165480' => 'chi', 'CARHR194190' => 'chi', 'Carub.0001s4381' => 'cru', 'Carub.0003s1131' => 'cru', 'Carub.0003s1305' => 'cru', 'Carub.0005s2218' => 'cru', 'Carub.0006s1711' => 'cru', 'Ca_05894_v3' => 'car', 'Ca_16379_v3' => 'car', 'Ca_21557_v3' => 'car', 'Ca_25941_v3' => 'car', 'CBR_g34152' => 'cbr', 'CBR_g49492' => 'cbr', 'Cc00_g26120' => 'ccan', 'Cc01_g02150' => 'ccan', 'Cc02_g07770' => 'ccan', 'Cc03_g02570' => 'ccan', 'CDE02G1118' => 'cde', 'CDE05G2235' => 'cde', 'CDE11G0545' => 'cde', 'CDE11G1051' => 'cde', 'Cfa001184' => 'cfa', 'Cfa001468' => 'cfa', 'Cfa009701' => 'cfa', 'Cfa020116' => 'cfa', 'Cfa020117' => 'cfa', 'Ciclev10005625m.g' => 'ccl', 'Ciclev10012758m.g' => 'ccl', 'Ciclev10016371m.g' => 'ccl', 'Ciclev10032342m.g' => 'ccl', 'CiPaw.01G155400' => 'cil', 'CiPaw.01G288100' => 'cil', 'CiPaw.02G088000' => 'cil', 'CiPaw.02G184600' => 'cil', 'CiPaw.10G023800' => 'cil', 'CiPaw.13G175500' => 'cil', 'CiPaw.14G135100' => 'cil', 'ClCG03G012340' => 'cla', 'ClCG05G005700' => 'cla', 'ClCG07G003240' => 'cla', 'ClCG10G017790' => 'cla', 'COL.COLO4_29433' => 'col', 'Cpa.g.sc1.413' => 'cpa', 'Cpa.g.sc119.64' => 'cpa', 'Cpa.g.sc16.86' => 'cpa', 'Cpa.g.sc85.26' => 'cpa', 'Cre01.g038650' => 'cre', 'Cre13.g573650' => 'cre', 'Cre13.g586916' => 'cre', 'CsaV3_1G043660' => 'csa', 'CsaV3_3G014050' => 'csa', 'CsaV3_3G038510' => 'csa', 'CsaV3_5G007990' => 'csa', 'CsaV3_7G005550' => 'csa', 'CSS0007163' => 'camsi', 'CSS0026311' => 'camsi', 'CSS0030335' => 'camsi', 'CSS0043084' => 'camsi', 'DCAR_003304' => 'dca', 'DCAR_011710' => 'dca', 'DCAR_023815' => 'dca', 'Dinv13450' => 'din', 'Dinv24032' => 'din', 'Dinv26023' => 'din', 'Duzib093G1381' => 'dzi', 'Duzib114G0871' => 'dzi', 'Duzib128G1943' => 'dzi', 'Duzib150G0274' => 'dzi', 'Duzib151G0792' => 'dzi', 'Duzib168G0268' => 'dzi', 'Duzib212G0373' => 'dzi', 'ECA232G4386' => 'eca', 'ECA232G4424' => 'eca', 'ECA233G5876' => 'eca', 'ECA238G1495' => 'eca', 'ECA248G1698' => 'eca', 'ECA248G3711' => 'eca', 'EL10Ac2g04740' => 'bvu', 'EL10Ac3g06849' => 'bvu', 'EL10Ac4g10368' => 'bvu', 'Eucgr.A02501' => 'egr', 'Eucgr.A02506' => 'egr', 'Eucgr.B01229' => 'egr', 'Eucgr.B01231' => 'egr', 'Eucgr.J00004' => 'egr', 'Eucgr.J01814' => 'egr', 'Eucgr.J01817' => 'egr', 'Eucgr.L01219' => 'egr', 'FAN02G3873' => 'fan', 'FAN05G0318' => 'fan', 'FAN05G1894' => 'fan', 'FAN07G0347' => 'fan', 'FAN12G2571' => 'fan', 'FAN12G3440' => 'fan', 'FAN14G0675' => 'fan', 'FAN17G2094' => 'fan', 'FAN22G0118' => 'fan', 'FvH4_3g45331' => 'fve', 'FvH4_4g16920' => 'fve', 'FvH4_6g21490' => 'fve', 'FvH4_7g22601' => 'fve', 'FvH4_7g22602' => 'fve', 'Glyma.02G220800' => 'gma', 'Glyma.02G247800' => 'gma', 'Glyma.07G252700' => 'gma', 'Glyma.09G104200' => 'gma', 'Glyma.14G068500' => 'gma', 'Glyma.14G188200' => 'gma', 'Glyma.17G021700' => 'gma', 'Gohir.A04G054300' => 'ghi', 'Gohir.A06G103300' => 'ghi', 'Gohir.A06G167300' => 'ghi', 'Gohir.A09G130200' => 'ghi', 'Gohir.A10G103700' => 'ghi', 'Gohir.A10G220000' => 'ghi', 'Gohir.D04G094100' => 'ghi', 'Gohir.D06G111000' => 'ghi', 'Gohir.D06G172700' => 'ghi', 'Gohir.D10G164700' => 'ghi', 'Gohir.D10G229500' => 'ghi', 'Gorai.009G393200' => 'gra', 'Gorai.010G126300' => 'gra', 'Gorai.010G201600' => 'gra', 'Gorai.011G183900' => 'gra', 'Gorai.011G262000' => 'gra', 'GSVIVG01001344001' => 'vvi', 'GSVIVG01016562001' => 'vvi', 'GSVIVG01022010001' => 'vvi', 'GSVIVG01025432001' => 'vvi', 'HanXRQChr01g0021651' => 'han', 'HanXRQChr03g0073721' => 'han', 'HanXRQChr07g0201281' => 'han', 'HanXRQChr09g0259771' => 'han', 'HanXRQChr10g0315341' => 'han', 'HanXRQChr11g0344731' => 'han', 'HanXRQChr11g0344741' => 'han', 'HanXRQChr13g0397791' => 'han', 'HanXRQChr13g0405311' => 'han', 'HanXRQChr14g0437721' => 'han', 'Haze_01033' => 'cav', 'Haze_01034' => 'cav', 'Haze_17074' => 'cav', 'Haze_20071' => 'cav', 'Hma1.2p1_0116F.1_g056240' => 'hma', 'Hma1.2p1_0159F.1_g070485' => 'hma', 'Hma1.2p1_0241F.1_g100610' => 'hma', 'Hma1.2p1_0325F.1_g125900' => 'hma', 'Hma1.2p1_0508F.1_g168770' => 'hma', 'Hma1.2p1_0643F.1_g194620' => 'hma', 'Hma1.2p1_0953F.1_g241130' => 'hma', 'Hma1.2p1_1671F.1_g296705' => 'hma', 'HPP92_015936' => 'vpl', 'HPP92_017193' => 'vpl', 'HPP92_017553' => 'vpl', 'HPP92_027339' => 'vpl', 'Hund07582' => 'sun', 'Hund13768' => 'sun', 'Hund16456' => 'sun', 'Hund24826' => 'sun', 'Hund24897' => 'sun', 'Lalb_Chr02g0153871' => 'lal', 'Lalb_Chr02g0153881' => 'lal', 'Lalb_Chr04g0251241' => 'lal', 'Lalb_Chr04g0251251' => 'lal', 'Lalb_Chr07g0177531' => 'lal', 'Lalb_Chr08g0230311' => 'lal', 'Lalb_Chr10g0104541' => 'lal', 'Lalb_Chr13g0303951' => 'lal', 'Lalb_Chr17g0346201' => 'lal', 'Lalb_Chr23g0278461' => 'lal', 'Lj1A1135T85' => 'lonja', 'Lj1A939G60' => 'lonja', 'Lj1C542G3' => 'lonja', 'Lj4g0004311' => 'lja', 'Lj5g0005013' => 'lja', 'Lj5g0017417' => 'lja', 'Lj6C179T4' => 'lonja', 'Lj6g0024150' => 'lja', 'Lj8C83T18' => 'lonja', 'LjContig00141g0012425' => 'lja', 'Lsat_1_v5_gn_1_58760' => 'lsa', 'Lsat_1_v5_gn_2_119240' => 'lsa', 'Lsat_1_v5_gn_2_53461' => 'lsa', 'Lsat_1_v5_gn_4_137260' => 'lsa', 'Lsat_1_v5_gn_6_54241' => 'lsa', 'Manes.03G189500' => 'mes', 'Manes.07G116804' => 'mes', 'Manes.09G040200' => 'mes', 'Manes.10G029600' => 'mes', 'Manes.15G107000' => 'mes', 'Mapoly0098s0012' => 'mpo', 'MBI05_g22024_MAGBIO' => 'mbi', 'MBI18_g15801_MAGBIO' => 'mbi', 'MCO03G279' => 'mco', 'MCO04G238' => 'mco', 'MD01G1135000' => 'mdo', 'MD03G1005800' => 'mdo', 'MD07G1199700' => 'mdo', 'MD11G1008700' => 'mdo', 'MD11G1008800' => 'mdo', 'MD13G1175700' => 'mdo', 'MD14G1050400' => 'mdo', 'MD14G1050500' => 'mdo', 'MD16G1177500' => 'mdo', 'Medtr1g054675' => 'mtr', 'Medtr3g083550' => 'mtr', 'Medtr4g118630' => 'mtr', 'Medtr5g079870' => 'mtr', 'MELO3C006598.2' => 'cme', 'MELO3C009595.2' => 'cme', 'MELO3C015085.2' => 'cme', 'MELO3C023845.2' => 'cme', 'Migut.D02546' => 'egut', 'Migut.G00230' => 'egut', 'Migut.J01877' => 'egut', 'Migut.N00132' => 'egut', 'Migut.N00566' => 'egut', 'MSTRG.10855' => 'ama', 'MSTRG.20944' => 'ama', 'MSTRG.21823' => 'ama', 'Nitab4.5_0000658g0110' => 'nta', 'Nitab4.5_0001059g0180' => 'nta', 'Nitab4.5_0001730g0110' => 'nta', 'Nitab4.5_0002532g0050' => 'nta', 'Nn2g11117' => 'nnu', 'Nn2g12627' => 'nnu', 'Nn2g13353' => 'nnu', 'Nn4g26085' => 'nnu', 'Oeu010958.2' => 'oeu', 'Oeu024296.1' => 'oeu', 'Oeu027221.2' => 'oeu', 'Oeu033919.1' => 'oeu', 'Oeu035959.1' => 'oeu', 'Oeu053382.1' => 'oeu', 'Oeu057597.1' => 'oeu', 'Oeu058888.2' => 'oeu', 'Oeu059673.1' => 'oeu', 'Os02g0252100' => 'osa', 'Os03g0363800' => 'osa', 'Os03g0374575' => 'osa', 'Os07g0633200' => 'osa', 'Os11g0704700' => 'osa', 'Os12g0572300' => 'osa', 'Os12g0572400' => 'osa', 'Peaxi162Scf00349g00096' => 'pax', 'Peaxi162Scf00463g00214' => 'pax', 'PGR004G0332' => 'pgr', 'PGR044G0210' => 'pgr', 'PGR119G0664' => 'pgr', 'PGSC0003DMG400004273' => 'stu', 'PGSC0003DMG400006298' => 'stu', 'PGSC0003DMG400032132' => 'stu', 'Phvul.001G268900' => 'pvu', 'Phvul.003G099500' => 'pvu', 'Phvul.007G145300' => 'pvu', 'Phvul.007G262600' => 'pvu', 'Phvul.008G232900' => 'pvu', 'Potri.001G006400' => 'ptr', 'Potri.003G218600' => 'ptr', 'Potri.006G197000' => 'ptr', 'Potri.008G056600' => 'ptr', 'Potri.008G196700' => 'ptr', 'Potri.010G026100' => 'ptr', 'Potri.010G203200' => 'ptr', 'Potri.016G062500' => 'ptr', 'Pp3c5_15600' => 'ppa', 'Pp3c5_15610' => 'ppa', 'Pp3c6_9110' => 'ppa', 'Pp3s152_10' => 'ppa', 'PRCOL_00002175' => 'pco', 'Prupe.1G144400' => 'ppe', 'Prupe.2G236400' => 'ppe', 'Prupe.6G005600' => 'ppe', 'Prupe.7G085400' => 'ppe', 'Psat2g041600' => 'psa', 'Psat4g030000' => 'psa', 'Psat5g100960' => 'psa', 'Psat6g090800' => 'psa', 'PSO151G0147' => 'pso', 'PSO170G5418' => 'pso', 'PSO210G7442' => 'pso', 'PSO251G0002' => 'pso', 'PSO302G0119' => 'pso', 'PSO339G0614' => 'pso', 'PSO339G6098' => 'pso', 'PSO384G1488' => 'pso', 'PSO832G3799' => 'pso', 'QL01p008467' => 'qlo', 'QL06p006724' => 'qlo', 'QL07p025482' => 'qlo', 'QL08p059648' => 'qlo', 'RcHm_v2.0_Chr1g0367721' => 'rch', 'RcHm_v2.0_Chr3g0478671' => 'rch', 'RcHm_v2.0_Chr4g0420501' => 'rch', 'RcHm_v2.0_Chr5g0083131' => 'rch', 'Rhsim03G0130000' => 'rsi', 'Rhsim04G0093600' => 'rsi', 'Rhsim04G0214200' => 'rsi', 'Rhsim09G0166300' => 'rsi', 'RhsimUnG0042200' => 'rsi', 'Sabra03G0163000' => 'sbr', 'Sabra06G0151500' => 'sbr', 'Sabra08G0163500' => 'sbr', 'Sabra10G0013500' => 'sbr', 'Sabra16G0064400' => 'sbr', 'Sc09g0000140' => 'sci', 'Sc10g0001630' => 'sci', 'Sc13g0002520' => 'sci', 'Sc25g0004640' => 'sci', 'Sed0004317' => 'sed', 'Sed0005553' => 'sed', 'Sed0013318' => 'sed', 'Sed0023172' => 'sed', 'Sed0026175' => 'sed', 'SEGI_00523' => 'sgi', 'SEGI_12635' => 'sgi', 'SEGI_28874' => 'sgi', 'SEGI_36663' => 'sgi', 'SEGI_39452' => 'sgi', 'SEGI_41220' => 'sgi', 'SGA_v2.0_scaffold110G31321' => 'sas', 'SGA_v2.0_scaffold142G35673' => 'sas', 'SGA_v2.0_scaffold6G03285' => 'sas', 'SGA_v2.0_scaffold6G03419' => 'sas', 'SHI00327' => 'shi', 'SMO147G0407' => 'smo', 'SMO358G0110' => 'smo', 'SMO358G0425' => 'smo', 'Solyc01g005820.4' => 'sly', 'Solyc01g080660.3' => 'sly', 'Sopen01g001820' => 'spe', 'Sopen01g030850' => 'spe', 'Sopen12g035020' => 'spe', 'Sp1g40970' => 'spa', 'Sp3g10200' => 'spa', 'Sp3g11780' => 'spa', 'Sp5g07010' => 'spa', 'Sp6g25570' => 'spa', 'TAR362G1256' => 'tar', 'TAR369G1016' => 'tar', 'TAR625G0206' => 'tar', 'TAR633G1370' => 'tar', 'TAR633G1703' => 'tar', 'TAR633G1837' => 'tar', 'TAR636G1482' => 'tar', 'TAR636G2521' => 'tar', 'THA.LOC104799276' => 'tha', 'THA.LOC104807945' => 'tha', 'THA.LOC104810033' => 'tha', 'THA.LOC104815664' => 'tha', 'THA.LOC104818835' => 'tha', 'THA.LOC104822676' => 'tha', 'Thecc.04G274400' => 'tca', 'Thecc.05G180100' => 'tca', 'Thecc.09G208600' => 'tca', 'Thecc.10G040700' => 'tca', 'Thhalv10010627m.g' => 'esa', 'Thhalv10011714m.g' => 'esa', 'Thhalv10015534m.g' => 'esa', 'Thhalv10021351m.g' => 'esa', 'Thhalv10021457m.g' => 'esa', 'TPR.G14494' => 'tpr', 'TPR.G14949' => 'tpr', 'TPR.G19317' => 'tpr', 'TPR.G3508' => 'tpr', 'TPR.G403' => 'tpr', 'TWI09G1539' => 'twi', 'TWI32G1002' => 'twi', 'TWI38G1186' => 'twi', 'TWI53G1669' => 'twi', 'TWI60G1426' => 'twi', 'TWI63G0311' => 'twi', 'TWI73G0638' => 'twi', 'vmacro07176' => 'vma', 'vmacro10229' => 'vma', 'vmacro12606' => 'vma', 'vmacro15277' => 'vma', 'vmacro22126' => 'vma', 'VMungo0647G0607' => 'vmu', 'VMungo0720G0721' => 'vmu', 'VMungo1215G1875' => 'vmu', 'VMungo1383G1868' => 'vmu', 'Zm00001eb017780' => 'zma', 'Zm00001eb018140' => 'zma', 'Zm00001eb029330' => 'zma', 'Zm00001eb082450' => 'zma', 'Zm00001eb088980' => 'zma', 'Zm00001eb134410' => 'zma', 'Zm00001eb155840' => 'zma', 'Zm00001eb164590' => 'zma', 'Zm00001eb220130' => 'zma', 'Zm00001eb267400' => 'zma', 'Zm00001eb305510' => 'zma', 'Zm00001eb328450' => 'zma', 'Zm00001eb336060' => 'zma', 'Zm00001eb348570' => 'zma', 'Zm00001eb354330' => 'zma', 'Zm00001eb394060' => 'zma' ) $gf_id = 'HOM05D001283' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001283' ) $data_identifier = 'HOM05D001283' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 8, 'bol' => (int) 8, 'bra' => (int) 7, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 7, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 4, 'cre' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 9, 'fve' => (int) 5, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 5, 'lal' => (int) 10, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 4, 'nnu' => (int) 4, 'oeu' => (int) 9, 'osa' => (int) 7, 'pax' => (int) 2, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 9, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 6, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 7, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394060' $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